The device was found at the front door of St Mary's on the Hill on the Carnmoney Road shortly after 10pm on Saturday.
The road was closed for a number of hours while army bomb experts made the bomb safe. It was described as "small, crude but viable", safe.
Father Damian McCaughan is a curate at the church. His home, and others nearby, were evacuated during the alert.
"It's a great shame. This is an area where the different church communities have come together a lot in recent years and relationships between ourselves and the other churches are excellent," he said.
"It's a great shame that something like this should spoil perhaps the good relationships but we are still confident that this does not reflect any of the communities in Newtownabbey and we've to continue the good work of building up relationships."
The device has been taken away for further examination.
At Mass on Sunday morning, parishioners said they could not understand why the church was targeted.
"I'm shocked at the fact that something like this could happen in the middle of our community. It does not help anyone," said Kevin Denvir.
"We thought we had left all this behind. We have moved on in Glengormley yet we still have incidents like this happening."
Gerry O'Reilly, a local Sinn Féin councillor, said: "Last night's attack on St Mary's on the Hill was the latest in a series of despicable sectarian acts against the church and this community
"Those involved must be condemned by the whole community and be swiftly brought before the courts.
"Anyone who believes it is ok to attack a place of worship is clearly a danger to the public and must be taken off the streets."
Paula Bradley, DUP MLA for north Belfast, described the targeting of a church as "abhorrent".
"This is not wanted in Newtownabbey and there is no justification for such attacks.
"Whatever cause those behind it sought to advance they will only strengthen the resolve of the local community not to tolerate such acts of intimidation.
"There have been a series of hoax and viable devices planted in Newtownabbey over recent weeks. This madness must come to an end," she added.
Police have appealed for anyone who noticed suspicious activity in the area to come forward.